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NMR assignments of the N-terminal domain of Staphylococcus aureus hibernation promoting factor (SaHPF)

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Abstract

Staphylococcus aureus: hibernation-promoting factor (SaHPF) is a 22.2 kDa stationary-phase protein that binds to the ribosome and turns it to the inactive form favoring survival under stress. Sequence analysis has shown that this protein is combination of two homolog proteins obtained in Escherichia coli—ribosome hibernation promoting factor (HPF) (11,000 Da) and ribosome modulation factor RMF (6500 Da). Binding site of E. coli HPF on the ribosome have been shown by X-ray study of Thermus thermophilus ribosome complex. Hence, recent studies reported that the interface is markedly different between 100S from S. aureus and E. coli. Cryo-electron microscopy structure of 100S S. aureus ribosomes reveal that the SaHPF-NTD binds to the 30S subunit as observed for shorter variants of HPF in other species and the C-terminal domain (CTD) protrudes out of each ribosome in order to mediate dimerization. SaHPF-NTD binds to the small subunit similarly to its homologs EcHPF, EcYfiA, and a plastid-specific YfiA. Furthermore, upon binding to the small subunit, the SaHPF-NTD occludes several antibiotic binding sites at the A site (hygromycin B, tetracycline), P site (edeine) and E site (pactamycin, kasugamycin). In order to elucidate the structure, dynamics and function of SaHPF-NTD from S. aureus, here we report the backbone and side chain resonance assignments for SaHPF-NTD. Analysis of the backbone chemical shifts by TALOS+ suggests that SaHPF-NTD contains two α-helices and four β-strands (β1-α1-β2-β3-β4-α2 topology). Investigating the long-term survival of S. aureus and other bacteria under antibiotic pressure could lead to advances in antibiotherapy.

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Abbreviations

IPTG:

Isopropyl-thio-β-d-galactoside

S. aureus :

Staphylococcus aureus

RMF:

Ribosome modulation factor

SaHPF:

Staphylococcus aureus hibernation promoting factor

SaHPF-NTD:

N-terminal domain of SaHPF

SaHPF-CTD:

C-terminal domain of SaHPF

Cryo-EM:

Cryo-electron microscopy

PIC:

Protease inhibitor cocktail

PMSF:

Phenylmethane sulfonyl fluoride

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Acknowledgements

This work was supported by the Russian Science Foundation (Grant 16-14-10014).

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Authors and Affiliations

  1. NMR laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, 18 Kremlevskaya, Kazan, Russian Federation, 420008

    Konstantin S. Usachev

  2. Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlevskaya, Kazan, Russian Federation, 420008

    Konstantin S. Usachev, Rustam Kh. Ayupov, Shamil Z. Validov, Iskander Sh. Khusainov & Marat M. Yusupov

  3. Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France

    Iskander Sh. Khusainov & Marat M. Yusupov

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  1. Konstantin S. Usachev
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  2. Rustam Kh. Ayupov
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  3. Shamil Z. Validov
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  4. Iskander Sh. Khusainov
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  5. Marat M. Yusupov
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Correspondence to Konstantin S. Usachev.

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Usachev, K.S., Ayupov, R.K., Validov, S.Z. et al. NMR assignments of the N-terminal domain of Staphylococcus aureus hibernation promoting factor (SaHPF). Biomol NMR Assign 12, 85–89 (2018). https://doi.org/10.1007/s12104-017-9783-2

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